First off, the directory structure described in the guide, with 'apps' and 'uploads' is unnecessary. All you need is a directory that contains your Packages.gz file and a subdirectory named 'deb' that holds your package. If you keep the directory structure from the guide, your Cydia URL will be http://yoursite.com/cydia/upload, which is tacky.
More importantly, if you follow the guide, your app will not install to the /Applications directory of your iOS device, and any *.info files will be broken, which was very bad news for RetroArch. To fix this, I followed this guide, the important parts from which I will summarize here:
First, you'll need to take create a new directory with the same name as your application--in my case, RetroArch. Then, inside that directory, create another new directory named Applications and one named DEBIAN. In the DEBIAN directory, place your 'control' file, which contains information about your application, and in the Applications directory, place your compiled application (in my case RetroArch.app).
At this point, you're ready to bundle your application using dpkg:
dpkg -b [your.app.name]Once your deb is created, you can delete the directory structure and then create your Packages.gz:
dpkg-scanpackages -m . /dev/null | gzip -9c >Packages.gzCreate a directory called 'deb' and drop your deb bundle into it and you should be all set.